GapMind for catabolism of small carbon sources


D-glucose-6-phosphate catabolism

Analysis of pathway glucose-6-P in 201 genomes

Genome Best path
Acidimicrobium ferrooxidans DSM 10331 uhpT
Acidithiobacillus ferrooxidans ATCC 23270 uhpT
Acidovorax sp. GW101-3H11 uhpT
Algiphilus aromaticivorans DG1253 uhpT
Alicycliphilus denitrificans K601 uhpT
Alkalihalobacterium alkalinitrilicum DSM 22532 uhpT
Allochromatium vinosum DSM 180 uhpT
Ammonifex degensii KC4 uhpT
Anaerobutyricum hallii DSM 3353 uhpT
Aquimarina longa SW024 uhpT
Archaeoglobus veneficus SNP6 uhpT
Arcobacter nitrofigilis DSM 7299 uhpT
Azoarcus olearius BH72 uhpT
Azohydromonas australica DSM 1124 uhpT
Azorhizobium caulinodans ORS 571 uhpT
Azospirillum brasilense Sp245 uhpT
Azospirillum sp. B510 uhpT
Bacteroides thetaiotaomicron VPI-5482 uhpT
Beijerinckia indica ATCC 9039 uhpT
Beijerinckia mobilis UQM 1969 uhpT
Billgrantia desiderata SP1 uhpT
Bradyrhizobium sp. BTAi1 uhpT
Brevundimonas sp. GW460-12-10-14-LB2 uhpT
Burkholderia phytofirmans PsJN uhpT
Burkholderia vietnamiensis G4 uhpT
Calditerrivibrio nitroreducens DSM 19672 uhpT
Caminibacter mediatlanticus TB-2 uhpT
Carboxydothermus pertinax Ug1 uhpT
Caulobacter crescentus NA1000 uhpT
Cereibacter sphaeroides ATCC 17029 uhpT
Chlorobaculum parvum NCIB 8327 uhpT
Chlorobaculum tepidum TLS uhpT
Chlorobium limicola DSM 245 uhpT
Chlorobium phaeobacteroides BS1 uhpT
Clostridium acetobutylicum ATCC 824 uhpT
Clostridium kluyveri DSM 555 uhpT
Clostridium tyrobutyricum FAM22553 uhpT
Crocosphaera subtropica ATCC 51142 uhpT
Cupriavidus basilensis FW507-4G11 uhpT
Dechloromonas agitata is5 uhpT
Dechlorosoma suillum PS uhpT
Dehalococcoides mccartyi 195 uhpT
Denitrovibrio acetiphilus DSM 12809 uhpT
Derxia gummosa DSM 723 uhpT
Desulfacinum hydrothermale DSM 13146 uhpT
Desulfacinum infernum DSM 9756 uhpT
Desulfarculus baarsii DSM 2075 uhpT
Desulfatibacillum aliphaticivorans DSM 15576 uhpT
Desulfatiglans anilini DSM 4660 uhpT
Desulfitobacterium hafniense DCB-2 uhpT
Desulfobacca acetoxidans DSM 11109 uhpT
Desulfobacter vibrioformis DSM 8776 uhpT
Desulfogranum mediterraneum DSM 13871 uhpT
Desulforamulus ruminis DSM 2154 uhpT
Desulfoscipio geothermicus DSM 3669 uhpT
Desulfotalea psychrophila LSv54 uhpT
Desulfovibrio oxyclinae DSM 11498 uhpT
Desulfovibrio vulgaris Hildenborough JW710 uhpT
Desulfovibrio vulgaris Miyazaki F uhpT
Desulfurobacterium atlanticum DSM 15668 uhpT
Desulfuromonas acetexigens uhpT
Desulfuromusa kysingii DSM 7343 uhpT
Dinoroseobacter shibae DFL-12 uhpT
Dyella japonica UNC79MFTsu3.2 uhpT
Echinicola vietnamensis KMM 6221, DSM 17526 uhpT
Escherichia coli BW25113 uhpT
Ferroglobus placidus DSM 10642 uhpT
Frankia alni ACN14a uhpT
Geobacter metallireducens GS-15 uhpT
Geotalea uraniireducens Rf4 uhpT
Halococcus hamelinensis 100A6 uhpT
Haloechinothrix alba DSM 45207 uhpT
Haloferax volcanii DS2 uhpT
Haloglycomyces albus DSM 45210 uhpT
Halorhodospira halophila SL1 uhpT
Heliomicrobium modesticaldum Ice1; ATCC 51547 uhpT
Herbaspirillum autotrophicum IAM 14942 uhpT
Herbaspirillum seropedicae SmR1 uhpT
Hippea alviniae EP5-r uhpT
Hydrogenophaga taeniospiralis NBRC 102512 uhpT
Hydrogenovibrio halophilus DSM 15072 uhpT
Hydrogenovibrio kuenenii DSM 12350 uhpT
Hydrogenovibrio marinus DSM 11271 uhpT
Hyphomicrobium sulfonivorans WDL6 uhpT
Klebsiella michiganensis M5al uhpT
Klebsiella variicola At-22 uhpT
Kyrpidia tusciae DSM 2912 uhpT
Leptospirillum ferrooxidans C2-3 uhpT
Magnetospirillum magneticum AMB-1 uhpT
Malonomonas rubra DSM 5091 uhpT
Maridesulfovibrio bastinii DSM 16055 uhpT
Maridesulfovibrio zosterae DSM 11974 uhpT
Marinobacter adhaerens HP15 uhpT
Mesorhizobium ciceri WSM1271 uhpT
Methanobacterium lacus AL-21 uhpT
Methanococcus aeolicus Nankai-3 uhpT
Methanococcus maripaludis C5 uhpT
Methanosarcina acetivorans C2A uhpT
Methanosarcina mazei Go1 uhpT
Methanospirillum lacunae Ki8-1 uhpT
Methanothermobacter thermautotrophicus Delta H uhpT
Methylobacterium nodulans ORS 2060 uhpT
Methylobacterium sp. 4-46 Apr-46 uhpT
Methylocapsa acidiphila B2 uhpT
Methylocapsa aurea KYG uhpT
Methylocella silvestris BL2 uhpT
Methylococcus capsulatus Bath uhpT
Methylocystis bryophila S285 uhpT
Methyloferula stellata AR4T uhpT
Methylohalobius crimeensis 10Ki uhpT
Methylomonas methanica MC09 uhpT
Methylosarcina fibrata AML-C10 uhpT
Methylotuvimicrobium alcaliphilum 20Z uhpT
Methylovulum miyakonense HT12 uhpT
Mycolicibacterium vanbaalenii PYR-1 uhpT
Nitratifractor salsuginis DSM 16511 uhpT
Nitratiruptor tergarcus DSM 16512 uhpT
Nitriliruptor alkaliphilus DSM 45188 uhpT
Nocardioides dokdonensis FR1436 uhpT
Nocardiopsis lucentensis DSM 44048 uhpT
Nostoc punctiforme ATCC 29133; PCC 73102 uhpT
Novosphingobium aromaticivorans DSM 12444 uhpT
Oleispira antarctica uhpT
Paraburkholderia atlantica CCGE1002 uhpT
Paraburkholderia bryophila 376MFSha3.1 uhpT
Paraburkholderia phymatum STM815 uhpT
Paucidesulfovibrio gracilis DSM 16080 uhpT
Pedobacter sp. GW460-11-11-14-LB5 uhpT
Pelobacter propionicus DSM 2379 uhpT
Persephonella marina EX-H1 uhpT
Phaeacidiphilus oryzae TH49 uhpT
Phaeobacter inhibens BS107 uhpT
Polaromonas naphthalenivorans CJ2 uhpT
Prosthecochloris aestuarii DSM 271 uhpT
Pseudarthrobacter sulfonivorans Ar51 uhpT
Pseudomonas benzenivorans DSM 8628 uhpT
Pseudomonas fluorescens FW300-N1B4 uhpT
Pseudomonas fluorescens FW300-N2C3 uhpT
Pseudomonas fluorescens FW300-N2E2 uhpT
Pseudomonas fluorescens FW300-N2E3 uhpT
Pseudomonas fluorescens GW456-L13 uhpT
Pseudomonas putida KT2440 uhpT
Pseudomonas simiae WCS417 uhpT
Pseudomonas stutzeri RCH2 uhpT
Pyrolobus fumarii 1A uhpT
Rhizobium etli CFN 42 uhpT
Rhizobium johnstonii 3841 uhpT
Rhizobium leguminosarum WSM1325 uhpT
Rhizorhabdus wittichii RW1 uhpT
Rhodanobacter denitrificans FW104-10B01 uhpT
Rhodomicrobium vannielii ATCC 17100 uhpT
Rhodopseudomonas palustris CGA009 uhpT
Rhodospirillum centenum SW; ATCC 51521 uhpT
Rhodospirillum rubrum ATCC 11170 uhpT
Roseburia faecis M72 uhpT
Saccharomonospora cyanea NA-134 uhpT
Sedimenticola selenatireducens DSM 17993 uhpT
Shewanella amazonensis SB2B uhpT
Shewanella loihica PV-4 uhpT
Shewanella oneidensis MR-1 uhpT
Shewanella sp. ANA-3 uhpT
Sinorhizobium fredii NGR234 uhpT
Sinorhizobium medicae WSM419 uhpT
Sinorhizobium meliloti 1021 uhpT
Sphingomonas koreensis DSMZ 15582 uhpT
Stenotrophomonas chelatiphaga DSM 21508 uhpT
Steroidobacter denitrificans DSM 18526 uhpT
Stutzerimonas stutzeri A1501 uhpT
Sulfuricurvum kujiense DSM 16994 uhpT
Sulfurihydrogenibium azorense Az-Fu1 uhpT
Sulfurihydrogenibium subterraneum DSM 15120 uhpT
Sulfurimonas denitrificans DSM 1251 uhpT
Sulfuritalea hydrogenivorans DSM 22779 uhpT
Sulfurivirga caldicuralii DSM 17737 uhpT
Synechococcus elongatus PCC 7942 uhpT
Teredinibacter turnerae T7901 uhpT
Thauera aminoaromatica S2 uhpT
Thermithiobacillus tepidarius DSM 3134 uhpT
Thermocrinis albus DSM 14484 uhpT
Thermodesulforhabdus norvegica DSM 9990 uhpT
Thermomonospora curvata DSM 43183 uhpT
Thermovibrio ammonificans HB-1 uhpT
Thermus aquaticus YT-1 uhpT
Thioalkalivibrio denitrificans ALJD uhpT
Thioalkalivibrio halophilus HL17 uhpT
Thioalkalivibrio paradoxus ARh 1 uhpT
Thioalkalivibrio thiocyanodenitrificans ARhD 1 uhpT
Thiohalomonas denitrificans HLD2 uhpT
Thiohalospira halophila HL 3 uhpT
Thiomicrorhabdus arctica DSM 13458 uhpT
Thiomicrorhabdus chilensis DSM 12352 uhpT
Thiomicrospira cyclica ALM1 uhpT
Thiomicrospira microaerophila ASL8-2 uhpT
Thiomicrospira pelophila DSM 1534 uhpT
Thiothrix lacustris DSM 21227 uhpT
Tistlia consotensis USBA 355 uhpT
Trichlorobacter lovleyi SZ uhpT
Trichodesmium erythraeum IMS101 Annotated Metagenome-Assembled Genome uhpT
Trichormus variabilis ATCC 29413 uhpT
Xanthobacter autotrophicus Py2 uhpT
Xenophilus azovorans DSM 13620 uhpT

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.



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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory